RBM18

Summary

RBM18 (RNA binding motif protein 18, HGNC:28413) is a protein-coding gene on chromosome 9q33.2, encoding Probable RNA-binding protein 18 (Q96H35). It is a selective cancer dependency (DepMap: 15.2% of cell lines).

Predicted to enable RNA binding activity. Located in cytosol; intercellular bridge; and nucleoplasm.

Source: NCBI Gene 92400 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 27 total
• Cancer dependency (DepMap): dependent in 15.2% of screened cell lines
• MANE Select transcript: NM_033117

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28413
Approved symbol	RBM18
Name	RNA binding motif protein 18
Location	9q33.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC2734
Ensembl gene	ENSG00000119446
Ensembl biotype	protein_coding
Entrez	92400

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 9 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000417201, ENST00000483428, ENST00000491850, ENST00000870815, ENST00000870816, ENST00000870817, ENST00000870818, ENST00000870819, ENST00000870820, ENST00000919715, ENST00000919718

RefSeq mRNA: 1 — MANE Select: NM_033117 NM_033117

CCDS: CCDS6839

Canonical transcript exons

ENST00000417201 — 6 exons

Exon	Start	End
ENSE00001695302	122264715	122264840
ENSE00001945206	122237622	122242043
ENSE00003655163	122261380	122261508
ENSE00003662821	122245256	122245341
ENSE00003676218	122251847	122251973
ENSE00003687045	122247518	122247604

Expression profiles

Bgee: expression breadth ubiquitous, 251 present calls, max score 96.79.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.2623 / max 109.1478, expressed in 1819 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
102390	28.5815	1819
102389	1.1785	808
102388	0.5023	263

Top tissues by expression

254 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
oocyte	CL:0000023	96.79	gold quality
tibialis anterior	UBERON:0001385	96.22	gold quality
secondary oocyte	CL:0000655	95.47	gold quality
left ventricle myocardium	UBERON:0006566	94.65	gold quality
deltoid	UBERON:0001476	94.44	gold quality
heart right ventricle	UBERON:0002080	93.54	gold quality
quadriceps femoris	UBERON:0001377	93.41	gold quality
vastus lateralis	UBERON:0001379	93.33	gold quality
myocardium	UBERON:0002349	93.24	gold quality
biceps brachii	UBERON:0001507	93.20	gold quality
cardiac muscle of right atrium	UBERON:0003379	93.02	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	92.20	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	91.58	gold quality
skeletal muscle tissue	UBERON:0001134	91.44	gold quality
muscle tissue	UBERON:0002385	91.21	gold quality
ganglionic eminence	UBERON:0004023	90.84	gold quality
cortical plate	UBERON:0005343	90.64	gold quality
ileal mucosa	UBERON:0000331	89.47	gold quality
hindlimb stylopod muscle	UBERON:0004252	89.47	gold quality
muscle of leg	UBERON:0001383	89.28	gold quality
gastrocnemius	UBERON:0001388	89.10	gold quality
islet of Langerhans	UBERON:0000006	88.59	gold quality
endothelial cell	CL:0000115	88.29	silver quality
stromal cell of endometrium	CL:0002255	87.81	gold quality
cardiac ventricle	UBERON:0002082	86.44	gold quality
heart left ventricle	UBERON:0002084	86.43	gold quality
smooth muscle tissue	UBERON:0001135	86.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.20	gold quality
prefrontal cortex	UBERON:0000451	86.16	gold quality
ventricular zone	UBERON:0003053	86.05	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.04

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

182 targeting RBM18, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-3658	99.96	73.87	4379

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 15.2% of screened cell lines.

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	rbm18	ENSDARG00000044255
mus_musculus	Rbm18	ENSMUSG00000026889
rattus_norvegicus	Rbm18	ENSRNOG00000006763
drosophila_melanogaster	CG14414	FBGN0030571

Protein

Protein identifiers

Probable RNA-binding protein 18 — Q96H35 (reviewed: Q96H35)

Alternative names: RNA-binding motif protein 18

All UniProt accessions (1): Q96H35

RefSeq proteins (1): NP_149108* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000504	RRM_dom	Domain
IPR012677	Nucleotide-bd_a/b_plait_sf	Homologous_superfamily
IPR035979	RBD_domain_sf	Homologous_superfamily
IPR039157	RBM18_RRM	Domain

Pfam: PF00076

UniProt features (3 total): chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96H35-F1	74.44	0.41

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 116 (showing top): GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, CREB_Q2_01, ATF4_Q2, CREBP1CJUN_01, CREB_01, CGTSACG_PAX3_B, TGACGTCA_ATF3_Q6, NUYTTEN_NIPP1_TARGETS_DN, CCGNMNNTNACG_UNKNOWN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A, LINDGREN_BLADDER_CANCER_CLUSTER_1_UP, GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN, BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS, STAT6_01

GO Biological Process (0):

GO Molecular Function (2): RNA binding (GO:0003723), nucleic acid binding (GO:0003676)

GO Cellular Component (3): nucleoplasm (GO:0005654), cytosol (GO:0005829), intercellular bridge (GO:0045171)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
nucleic acid binding	1
binding	1
nuclear lumen	1
cytoplasm	1

Protein interactions and networks

STRING

612 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
RBM18	FAM32A	Q9Y421	541
RBM18	SYF2	O95926	453
RBM18	RNF151	Q2KHN1	451
RBM18	UBOX5	O94941	450
RBM18	SUPT7L	O94864	447
RBM18	SYDE2	Q5VT97	440
RBM18	CFAP97	Q9P2B7	440
RBM18	GTF3C5	Q9Y5Q8	424
RBM18	CMTR1	Q8N1G2	420
RBM18	DCTN3	O75935	418
RBM18	ZMAT2	Q96NC0	415
RBM18	CRIPT	Q9P021	401
RBM18	BEX5	Q5H9J7	397
RBM18	PPP1R7	Q15435	389
RBM18	OST4	P0C6T2	386

IntAct

9 interactions, top by confidence:

A	B	Type	Score
EPHA3	RBM18	psi-mi:“MI:0915”(physical association)	0.370
RBM18	NDUFAB1	psi-mi:“MI:0915”(physical association)	0.370
TAP2	RBM18	psi-mi:“MI:0915”(physical association)	0.370
GCNT3	RBM18	psi-mi:“MI:0915”(physical association)	0.370
RBM18	CLTRN	psi-mi:“MI:0915”(physical association)	0.370
RBM18	GSN	psi-mi:“MI:0914”(association)	0.350
RBM18	SYT1	psi-mi:“MI:0914”(association)	0.350

BioGRID (28): ACTA2 (Affinity Capture-MS), GSN (Affinity Capture-MS), TMOD2 (Affinity Capture-MS), UBR3 (Affinity Capture-MS), MINA (Affinity Capture-MS), CAPZA2 (Affinity Capture-MS), CNRIP1 (Affinity Capture-MS), MINA (Affinity Capture-MS), TMOD2 (Affinity Capture-MS), GSN (Affinity Capture-MS), CNRIP1 (Affinity Capture-MS), UBR3 (Affinity Capture-MS), ACTA2 (Affinity Capture-MS), RBM18 (Negative Genetic), GSN (Affinity Capture-MS)

ESM2 similar proteins: A2VDZ9, A4IGK3, A5GFS8, B2GV05, G3V9R8, O22969, O77768, O95232, O95292, P07910, P11031, P52756, P53999, P57060, Q08DJ0, Q0IIC4, Q1RMU5, Q24K03, Q32KT0, Q3SX41, Q3ZCC5, Q4R947, Q5R601, Q5R6D0, Q5R6W3, Q5R8W6, Q5RA82, Q5RAM8, Q5SUF2, Q5ZIA0, Q5ZK63, Q63396, Q642H2, Q6PH81, Q86SE5, Q8BTF8, Q91YE7, Q96H35, Q96JC9, Q99J36

Diamond homologs: A6NFN3, B0XS28, B5DF91, O43347, O60176, O94432, O95758, P17225, P23246, P26599, P28644, P30352, P32831, P48809, P60047, P60048, P60049, P60050, P70372, Q00438, Q01130, Q04047, Q04836, Q06A98, Q06AT9, Q07955, Q09511, Q0VCY7, Q13242, Q15233, Q1JPY8, Q1LZD9, Q24491, Q28IQ9, Q29099, Q3MHR5, Q3MHX3, Q3YLA6, Q3ZCC5, Q4KLH4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

27 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	19
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1075 predictions. Top by Δscore:

Variant	Effect	Δscore
9:122242042:CA:C	acceptor_gain	1.0000
9:122242044:C:CC	acceptor_gain	1.0000
9:122245250:TCTTA:T	donor_loss	1.0000
9:122245251:CTTA:C	donor_loss	1.0000
9:122245252:TTAC:T	donor_loss	1.0000
9:122245253:TA:T	donor_loss	1.0000
9:122245254:ACCTT:A	donor_loss	1.0000
9:122245255:C:CG	donor_loss	1.0000
9:122245337:TATCT:T	acceptor_gain	1.0000
9:122245339:TCTCT:T	acceptor_loss	1.0000
9:122245340:CT:C	acceptor_gain	1.0000
9:122245341:TCTGA:T	acceptor_loss	1.0000
9:122245342:C:CC	acceptor_gain	1.0000
9:122245342:CTG:C	acceptor_loss	1.0000
9:122245343:T:A	acceptor_loss	1.0000
9:122247513:CGTA:C	donor_loss	1.0000
9:122247514:GTAC:G	donor_loss	1.0000
9:122247515:TAC:T	donor_loss	1.0000
9:122247516:ACCTT:A	donor_loss	1.0000
9:122247517:CCT:C	donor_gain	1.0000
9:122247601:CTTC:C	acceptor_gain	1.0000
9:122247603:TC:T	acceptor_gain	1.0000
9:122247604:CC:C	acceptor_gain	1.0000
9:122247605:C:CC	acceptor_gain	1.0000
9:122247606:T:C	acceptor_loss	1.0000
9:122247610:C:CT	acceptor_gain	1.0000
9:122247610:C:T	acceptor_gain	1.0000
9:122247611:A:T	acceptor_gain	1.0000
9:122251970:GTATC:G	acceptor_loss	1.0000
9:122251971:TATCT:T	acceptor_loss	1.0000

AlphaMissense

1234 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:122242008:A:G	L150P	1.000
9:122242010:T:A	K149N	1.000
9:122242010:T:G	K149N	1.000
9:122242015:C:G	A148P	1.000
9:122242020:A:T	I146N	1.000
9:122242024:C:G	A145P	1.000
9:122247540:C:G	R102P	1.000
9:122247543:A:T	V101E	1.000
9:122247549:A:G	L99P	1.000
9:122247564:G:T	A94D	1.000
9:122247579:A:G	L89P	1.000
9:122247591:G:T	A85D	1.000
9:122247592:C:G	A85P	1.000
9:122247601:C:G	A82P	1.000
9:122251860:A:G	F76S	1.000
9:122251866:A:T	V74D	1.000
9:122251868:A:C	F73L	1.000
9:122251868:A:T	F73L	1.000
9:122251869:A:C	F73C	1.000
9:122251869:A:G	F73S	1.000
9:122251870:A:C	F73V	1.000
9:122251870:A:G	F73L	1.000
9:122251870:A:T	F73I	1.000
9:122251871:A:C	C72W	1.000
9:122251872:C:T	C72Y	1.000
9:122251873:A:G	C72R	1.000
9:122251876:A:G	Y71H	1.000
9:122251878:C:A	G70V	1.000
9:122251878:C:T	G70D	1.000
9:122251879:C:G	G70R	1.000

dbSNP variants (sampled 300 via entrez): RS1000046070 (9:122244144 A>T), RS1000177950 (9:122253005 C>A,T), RS1000287105 (9:122257114 C>T), RS1000350388 (9:122264147 T>C), RS1000425441 (9:122263860 T>C), RS1000469272 (9:122257245 C>A), RS1000513900 (9:122255817 G>A,C), RS1000573854 (9:122257240 C>G), RS1000583539 (9:122255857 A>G), RS1000684752 (9:122262528 G>A), RS1000756767 (9:122262234 T>C), RS1001044238 (9:122238324 G>A), RS1001172832 (9:122258585 A>G), RS1001217233 (9:122262109 T>C), RS1001287127 (9:122258337 C>T)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Air Pollutants	affects expression, increases abundance, decreases expression	2
Valproic Acid	decreases expression, decreases methylation, increases expression	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	decreases expression	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
beta-methylcholine	affects expression	1
cylindrospermopsin	increases expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	increases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	increases expression	1
jinfukang	decreases expression	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Atrazine	increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	increases expression	1
Copper	decreases expression, affects binding	1
Demecolcine	increases expression	1
Disulfiram	affects binding, decreases expression	1
Doxorubicin	decreases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Hydrogen Peroxide	affects expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Methyl Methanesulfonate	increases expression	1
Ozone	increases abundance, affects expression	1
Phenobarbital	affects expression	1
Smoke	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.